The Histone Tail Codes

From Biomatics.org

The Histone tails can be thought of as fixed at one end and free to rotate about it's covalent bonds from the fixed end to the last carbon of the free end. Each rotating bond is some function of time. That is to say that from time zero onwards each covalent bond will be at some ramachandran angle...e.g. omega = f(t)). The state of the histone tail at any given time both influences the state of the histone core as well as being influenced by the activity of the histone core. One can therefore examine the complex pattern of the collection of omega functions OR one can simply look at the pattern formed by the last carbon of the free end. Following is one possible code: (0.01,0.0,0.01,1.5,2.5,0.0,1.5,2.5,0.0,1.5,2.5,0.0,1.5,2.5,0.0,1.5,2.5,0.0,1.5,0.01)... and it's resulting image. Note the use of numbers in the ratio of 5/3 ,,,representing the relative rotation rates... and the similarity to Da Vinci's Vitruvian Man..

Histone tails are highly flexible N- or C-terminal protrusions of histone proteins which facilitate the compaction of DNA into dense superstructures known as chromatin. On a molecular scale histone tails are polyelectrolytes with high degree of conformational disorder which allows them to function as biomolecular "switches", regulating various genetic processes. Unfortunately, their intrinsically disordered nature creates obstacles for comprehensive experimental investigation of both the structural and dynamical aspects of histone tails, because of which their conformational behaviors are still not well understood. In this work we have carried out ∼3 microsecond long all atom replica exchange molecular dynamics (REMD) simulations for each of four histone tails, H4, H3, H2B, and H2A, and probed their intrinsic conformational preferences. Our subsequent free energy landscape analysis demonstrated that most tails are not fully disordered, but show distinct conformational organization, containing specific flickering secondary structural elements. In particular, H4 forms β-hairpins, H3 and H2B adopt α-helical elements, while H2A is fully disordered. We rationalized observed patterns of conformational dynamics of various histone tails using ideas from physics of polyelectrolytes and disordered systems. We also discovered an intriguing re-entrant contraction-expansion of the tails upon heating, which is caused by subtle interplay between ionic screening and chain entropy.

Recent research indicates that epigenetic mechanisms and, in particular, the post-translational modification (PTM) of histones may contribute to memory encoding and storage. Among the dozens of possible histone PTMs, the methylation/demethylation of lysines in the N-terminal tail of histone H3 exhibits particularly strong links with cognitive abilities. First, the persistence and tight association with distinct transcriptional states of the gene make these modifications particularly suitable for being part of the molecular underpinnings of memory storage. Second, correlative evidence indicates that the methylation/demethylation of lysines in histone H3 is actively regulated during memory processes. Third, several enzymes regulating these PTMs are associated with intellectual disability disorders. We review here these three lines of evidence and discuss the potential role of epigenetic mechanisms centered on the methylation of lysine residues on histone H3 in neuroplasticity and neurodevelopmental disorders associated with intellectual disability.

...A number of studies in the last few years have indicated that memory consolidation for a particular task correlates with epigenetic modifications in the nucleus of neurons involved in the acquisition of that memory.

Structures and interactions of the core histone tail domains.

The core histone tail domains are "master control switches" that help define the structural and functional characteristics of chromatin at many levels. The tails modulate DNA accessibility within the nucleosome, are essential for stable folding of oligonucleosome arrays into condensed chromatin fibers, and are important for fiber-fiber interactions involved in higher order structures. Many nuclear signaling pathways impinge upon the tail domains, resulting in posttranslational modifications that are likely to alter the charge, structure, and/or interactions of the core histone tails or to serve as targets for the binding of ancillary proteins or other enzymatic functions. However, currently we have only a marginal understanding of the molecular details of core histone tail conformations and contacts. Here we review data related to the structures and interactions of the core histone tail domains and how these domains and posttranslational modifications therein may define the structure and function of chromatin.

Two Possible Types of Transition Functions

The transition functions for each covalent bond of each histone tail may be either discrete, continuous or combinations of both. As shown in the following table...

Or each bond is described as rotating at some continuous rate described as a function of time. The simplest type in this category would be each rate being some constant. In real life every third covalent bond in proteins is thought to be "fixed". This is not entirely accurate but does describe a possible subset of all the possibilities. So, for example, the bonds would be described as a set of relative angular rates of rotation. e.g. 5 3 0 5 3 0 5 3 0 etc. The possible combinations for even a protein of a few peptides is very large. For a protein of length one and integer rates up to 5 their are 5 times 5 or 25 possibilities. If we allow negative integers to -5 and 0 we have 11 times 11 or 121 possibilities.

The code sequence 0.002,0,0.002,2,1,0,2,1,0,2,4,0,2,4,0.004,2,4,4,0,2,4,0.002,1 yields the following skull like structure...